GDAL python scripts not importing in Linux

Question

I'm new to both GDAL and Linux. I have installed GDAL on my Linux mint PC. I am able to use regular GDAL commands in the terminal, but when I use python based commands,such as gdal_calc.py I get the following error:

Traceback (most recent call last):
  File "/usr/bin/gdal_calc.py", line 51, in <module>
    from osgeo import gdal
  File "/usr/lib/python2.7/dist-packages/osgeo/__init__.py", line 21, in <module>
    _gdal = swig_import_helper()
  File "/usr/lib/python2.7/dist-packages/osgeo/__init__.py", line 17, in swig_import_helper
    _mod = imp.load_module('_gdal', fp, pathname, description)
ImportError: /usr/lib/x86_64-linux-gnu/libspatialite.so.7: undefined symbol: freexl_version

I get the same error when I try from osgeo import gdal in a Python session. I am presuming that this has something to do with the locations of the gdal python scripts, or something related to spatialite (although I am not sure what spatialite has to do with this command). I also have QGIS and PostGIS installed, which presumably could cause some conflicts.

I have searched numerous sources, but can't find the cause of this error. I wonder if someone might be able to point me in the right direction.

Answer 1

Are you running the command directly (i.e ~/gdal_edit.py ) or are you passing the the script to the correct interpreter (i.e ~/bin/python3 gdal_edit.py) If I just run ~/gdal_edit.py I get a very similar error:

~/bin$ gdal_edit.py
Traceback (most recent call last):File "~/bin/gdal_edit.py", line 34, in <module> from osgeo import gdal
  File "~/lib/python3.6/site-packages/GDAL-2.2.1-py3.6-linux-x86_64.egg/osgeo/__init__.py", line 21, in <module>
_gdal = swig_import_helper()
  File "~/lib/python3.6/site-packages/GDAL-2.2.1-py3.6-linux-x86_64.egg/osgeo/__init__.py", line 17, in swig_import_helper
_mod = imp.load_module('_gdal', fp, pathname, description)
  File "~/lib/python3.6/site-packages/GDAL-2.2.1-py3.6-linux-x86_64.egg/osgeo/_gdal.py", line 7, in <module>
__bootstrap__()
  File "~/lib/python3.6/site-packages/GDAL-2.2.1-py3.6-linux-x86_64.egg/osgeo/_gdal.py", line 6, in __bootstrap__
imp.load_dynamic(__name__,__file__)
ImportError: ~/lib/python3.6/site-packages/GDAL-2.2.1-py3.6- 
linux-x86_64.egg/osgeo/_gdal.cpython-36m-x86_64-linux-gnu.so: undefined symbol: PyUnicode_AsUTF8String

But when I pass it the script to the interpreter:

  sguinn@zoot:~/bin$ ~/bin/python3 gdal_edit.py
Usage: gdal_edit [--help-general] [-ro] [-a_srs srs_def] [-a_ullr ulx uly lrx lry]
             [-tr xres yres] [-unsetgt] [-a_nodata value] [-unsetnodata]
             [-offset value] [-scale value]
             [-unsetstats] [-stats] [-approx_stats]
             [-gcp pixel line easting northing [elevation]]*
             [-unsetmd] [-oo NAME=VALUE]* [-mo "META-TAG=VALUE"]*  datasetname

Edit in place various information of an existing GDAL dataset.

It works as expected. Hope this helps